Many rice cultivars with numerous spikelets in a panicle (extra-heavy panicle types, EHPTs) have been developed to attain higher grain yield. However, there is a “grain-filling problem” for these EHPTs: they did not attain expected higher yield in many cases because of their low degree of grain filing, resulting from the increase in inferior spikelets showing poor grain filing. This short review addresses an approach toward the grain-filling problem of EHPT rice, particularly for the genetic improvement of its sink strength, and proposed two strategies for the resolution of this problem. The first strategy is the improvement of the poor grain filling in the increased inferior spikelets. This may be realized by utilizing suggested alleles for good grain filling at APS2, APL2 (they correspond to ADP-glucose pyrophosphorylase subunits), and SUT1 (sucrose transporter) loci. These alleles are expected to accelerate the unloading and metabolism of sucrose in developing endosperm, and to maintain a gradient of sucrose concentration from source to sink. The second strategy is the construction of a novel EHPT, in which its spikelet number is increased by increasing superior spikelets. A selection experiment strongly indicated that this strategy may be attained by the selection to increase the number of primary branches per panicle. Although these two strategies are needed to evaluate further, it is suggested that they are available to future breeding of EHPTs with good grain filling, and they can be combined with other approaches to this grain-filling problem.

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In organic cultivation of rice, application of rice bran to the surface of the paddy soil at the time of transplanting is adopted as one of the weeding techniques. In this study, we examined the effect of rice bran application for weeding on the growth of rice in relation to the formation of organic acid by rice bran application. Large-quantity application of bran (500g/m²; RB500) strongly reduced the redox potential in the soil and produced high concentrations of acetic acid and butyric acid in the soil compared to conventional-quantity application (100g/m²). RB500 delayed rooting and leaf age development, and suppressed the increase in stem number. The number of stems, which is a factor that greatly affects the yield, was strongly suppressed particularly in early- planting culture (May 11) compared to normal-planting culture (June 13), and the tendency of this result was not due to the age of seedlings used (young seedling with 3.2 leaf stage and middle seedling with 5.0 leaf stage). In the early- planting culture that the temperature was low at the time of transplanting, it was thought that the decomposition of rice bran was slow, and the presence of long-term harmful concentrations of organic acids affected the growth. From the view point of safe and stable rice production, we concluded that rice bran weeding combined with normal- planting culture is desirable.

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Although super-nodulating (SN) cultivars (cvs) of soybean had been developed for the improvement of seed yields of soybean, seed yields of all SN cvs developed until now were much less than those of normally nodulated soybean plants. The mechanism why plants of SN cv yielded less seed than those of normal nodulating cv was not clear yet. We compared the plant growth and seed productions from three genotypes of a near isogenic line (NIL) of soybean plants having different nodulation activities, i.e., Enrei (a popular cv in Japan), En-b0-1(a SN genotype produced from Enrei) and En1282 (a non-nodulating genotype produced from Enrei). We grew plants of them on soils in pot having low- and high-N levels to assess the effects of nodulation and volume of soil where plants can develop their roots since soil N inhibit the nodulation and N₂ fixation activities of soybean plants. We observed that plants from all the three genotypes showed almost the same seed weights per plant with each other except that of En1282 in low-N soil. Our potted experiment showed that higher N₂ fixation activity of En-b0-1 plants did not cause the decrease in seed weight per plant. Based on these results, it was suggested that the N₂ fixation activity of nodules was not a cause of poor seed productions in the SN genotype of soybean, En-b0-1, in fields.

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Prunus mume Sieb. et Zucc. (conventionally called Japanese apricot, Chinese mei and mume) is a deciduous fruit tree species in the genus Prunus. More than 300 P. mume cultivars are distributed mainly in East Asia, including Japanese fruit, small-fruit and ornamental cultivars and Taiwanese cultivars. In order to estimate demographic history of three Japanese and one Taiwanese subpopulations, approximate Bayesian computation analysis was carried out using 20 SSR genotype datasets of 53 cultivars (20 fruit, 8 small-fruit, 20 ornamental and 5 Taiwanese cultivars). At first, the best fitting model (posterior probability: 0.501) was estimated among six probable scenarios, and median values of demographic parameters were computed. The generation time for P. mume cultivars was assumed to be seven years (full reproductive age) for time conversion. In the best scenario, Japanese and Taiwanese populations had first diverged at 10360 (95% confidence interval (CI): 2079-56910) years ago, followed by the separation of ornamental cultivars among Japanese populations at 3633 (95% CI: 1218-12740) years ago, and final differentiation between fruit and small-fruit cultivars at 2387 (95% CI: 623-6258) years ago. Although the divergence times were roughly estimated, the results suggest that Japanese and Taiwanese populations were separated through the geographic isolation with different climate conditions, and ornamental, fruit and small-fruit cultivars were recently differentiated based on human preference in Japan.

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Fourteen accessions of African rice (Oryza glaberrima Steud.) were tested for their responses to complete submergence. In most accessions tested, submergence promoted shoot elongation and the survival rates after transfer to air were low. However, there were two accessions with relatively high survival rates (> 70%): one (C0025) induced shoot elongation by flooding and the other (C8567) not. The response of C8567 was similar to that of the O. sativa cultivar carrying the submergence-tolerance gene, SUB1A-1, but C8567 did not possess the gene. This suggests that the submergence tolerance of O. glaberrima should be elicited through a different mechanism from that of the tolerant O. sativa cultivar. An accession (C8834) carrying SUB1A-1 was found, which did not show submergence resistance with no expression of the gene. On the basis of morphological traits and DNA analysis of an O. glaberrima-specific gene, the possibility arises that C8834 may belong to O. sativa rather than O. glaberrima.

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Aromatic rice, a group of rice that emits a special aroma when cooked, has been cultivated in many regions throughout Japan and in many Asian countries for many years. We examined the sensory tests for judging the aroma of matured grains and fresh leaves (lamina) of aromatic rice varieties. In the boiled grain method, where the grains are boiled with water in a test tube. In the KOH leaf method, the leaves are sniffed for aroma 10 minutes after adding 10 ml of 1.7% KOH solution to 1 g of fine pieces of green leaf sample in a glass petri-dish. The 20 aromatic rice varieties showed a wide range of aroma strength in both boiled grain and KOH leaf method. The grain and leaf aroma strength were hardly affected by the fertilizer level and the grain aroma strength showed no clear tendency with the delay in the harvest time after heading among 9 aromatic rice varieties. The relationship between grain aroma and leaf aroma among 18 aromatic rice varieties was low. In conclusion, the KOH leaf method proved to be a rapid and accurate method to discriminate aromatic rice from non-aromatic rice.

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The Sandwich Method enables us to assay the allelopathic activity of the leaf litter of a donor plant inserted in agar medium, and evaluate the effects on the growth of the receptor plant. The allelopathic activity was determined as the percentage of growth of the radicle length of the receptor plant, lettuce (Lactuca sativa), grown in the agar medium containing the test plant leaf with that in the control medium containing agar only after 3 days at 20°C. We collected 29 plant species on 2nd February and 46 plant species on 28th June at the Yamashina Botanical Research Institute in Kyoto. Oxalis corniculate, Elaeocarpus zollingeri, Nageia nagi, Mucuna sempervirence, Atoropa belladonna, Moringa oleifera, Cinnamomum cassia, Pimenta dioica and Illicum anisatum showed very strong allelopathic activity; growth of radical length was suppressed to 8-30 ％ of that of the control. The plant species were medicinal plants, poisonous plants or oxalic-rich plants. Elucidation of the allelochemical is needed to make the allelopathy information useful to agriculture.

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Advances in sequencing technology and bioinformatic analyses enable the whole genomes of wheat and their wild ancestors to be decoded, making it easier to access full DNA sequence information that was previously fragmentary. This paper outlines difficulties in genome analysis of large and complex genomes in wheat species and presents the current status of genotyping research in wild relatives of wheat by RNA-Seq, a technique to avoid these difficulties.

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Various environmental factors including temperature and light are highly fluctuating under field condition. We established field transcriptomics that integrated massive transcriptome data under field conditions and corresponding meteorological data. Our large-scale field transcriptome study revealed that the majority of transcriptome dynamics could be explained by temperature and circadian clock and enabled us to predict transcriptome under given meteorological conditions.

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Recent advances in Next Generation Sequence (NGS) technology enable us to apply the bioinformatics to the field of crop research and breeding. However, because there are many hurdles to use NGS, such as skills of programing, knowledges of bioinformatics and preparation of computer facilities, experimental researchers and breeders can not use NGS easily. In this review, I introduce “Galaxy/NAAC”, that is a free web system to conduct data analysis maintained by Advanced Analysis Center, NARO (NAAC) and solves the hurdle of the bioinformatics against non-bioinformaticians.

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We surveyed historical changes of genetic backgrounds of Japanese rice cultivars, and revealed that the genetic diversity has been gradually decreasing, which is caused by consecutive inbreeding within the recent cultivars. To address expanding demands for new rice varieties in the near future, and to improve effciency of breeding selection in quantitative traits, sufficient genetic variation should be included in the breeding populations. As a trial of maximizing potential genetic variation in a crossed population, we develped a multiparental population derived from 8-way crosses. The population covered wide range of phenotypic diversity, and suggested a possibility of breaking the corelations between grain length and width. Additionaly, we are developing genome shuffling population which is expected to break the tight linkage drag, and evaluating tetraploid lines which might be used for introduction of useful genes from wide relatives or adjusting phenotypic values by regulation of dosage effect.

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